Variant report

Variant	rs9540942
Chromosome Location	chr13:67479075-67479076
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs12429002	1.00[YRI][hapmap]
rs12876382	1.00[YRI][hapmap]
rs1442005	0.84[MEX][hapmap]
rs1561769	1.00[YRI][hapmap]
rs17416460	0.89[CEU][hapmap]
rs1998606	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2119758	0.94[CEU][hapmap];0.89[GIH][hapmap];0.83[MEX][hapmap];0.91[TSI][hapmap];0.92[EUR][1000 genomes]
rs4884707	1.00[YRI][hapmap]
rs7350651	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9540924	0.82[EUR][1000 genomes]
rs9540934	0.89[CEU][hapmap];0.89[EUR][1000 genomes]
rs9540938	0.94[CEU][hapmap]
rs9540941	0.94[CEU][hapmap];0.97[EUR][1000 genomes]
rs956277	0.84[MEX][hapmap]
rs9564354	0.84[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1041133	chr13:66723731-67530595	Enhancers Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
2	nsv530605	chr13:67126136-67697306	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv1035741	chr13:67212973-68077950	Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv541817	chr13:67212973-68077950	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv523360	chr13:67322714-67520344	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv1051576	chr13:67322747-67520255	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv562136	chr13:67355618-67485147	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv900406	chr13:67434161-67532205	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	nsv900407	chr13:67434161-67603745	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	nsv562138	chr13:67455787-67511430	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
11	nsv832640	chr13:67460304-67635966	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:67474400-67485000	Weak transcription	Brain Hippocampus Middle	brain
2	chr13:67474600-67484000	Weak transcription	Brain Angular Gyrus	brain
3	chr13:67475200-67485200	Weak transcription	Brain Substantia Nigra	brain
4	chr13:67478400-67479800	Enhancers	iPS-18 Cell Line	embryonic stem cell
5	chr13:67478600-67479600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr13:67479000-67479400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr13:67479000-67479600	Enhancers	HUES64 Cell Line	embryonic stem cell
8	chr13:67479000-67480600	Enhancers	HUES48 Cell Line	embryonic stem cell

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dbSNP/dbVar ID: rs12345 /nsv7879
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chromosomal regions: chr1:12345-34567

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